The incorporation of [35S]sulphur in thiophenes by Tagetes patula roots was used as a model to study the regulation of secondary metabolism with a limited supply of substrate. Growth and thiophene accumulation were measured in root cultures incubated at various sulphate concentrations in the medium. A 20-fold to 40-fold reduction in the sulphate concentration did not affect elongation growth, branching and biomass production within 14 d but decreased the thiophene level to 25–50% of the control in the same period. The reduction in thiophene content was found to result from a decline in biosynthetic capacity of 80–95% after 8 d. This capacity was restored when roots were transferred to standard medium. The restoration took more than 24 h and was suppressed by cordycepin, an inhibitor of mRNA processing. It is concluded that the rate of thiophene synthesis is regulated by a control mechanism that reacts to the availability of sulphate to the roots.